<div dir="rtl"><div style="text-align: left; font-family: arial,helvetica,sans-serif;"><div dir="ltr" style="text-align: left;"><font size="2">Dear all,<br></font><font size="2">I am trying to run dynamics (mdrun) on GROMACS 4.5.3 in parallel on 8 processors, but it crashes after a while and refuses to reach to the end. <br>
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The error note that pops out is:<br> <br></font></div><div dir="ltr" style="text-align: left;"><font size="2">1 particles communicated to PME node 4 are more than 2/3 times the cut-off<br><br></font><font size="2">>> out of the domain decomposition cell of their charge group in dimension y.<br>
<br></font><font size="2">>> This usually means that your system is not well equilibrated<br><br></font><font size="2"><br></font><font size="2">My system contains protein, ATP and Mg. I have equilibirated it for 300 ps that were divided into 3 parts. <br>
</font><font size="2">The first 2 parts were the NVT equilibiration (the first one was made in order to </font><font size="2">equilibrate only the water) - 100 ps each.<br><br></font><font size="2"><br></font><font size="2">The third was the NPT - 100 ps.<br>
</font><font size="2">The system wasn't constraint.<br><br></font><font size="2">My mdp file is :<br></font><font size="2"> <br></font><font size="2">title = OPLS wt nbd1 MD <br></font><font size="2">; Run parameters<br>
</font><font size="2">integrator = md leap-frog integrator<br></font><font size="2">nsteps = 20000000 1 * 20000000 = 20000 ps, 20 ns<br><br></font><font size="2"><br></font><font size="2">dt = 0.001 1 fs<br></font><font size="2">; Output control<br>
</font><font size="2">nstxout = 20000 save coordinates every 2 ps<br></font><font size="2">nstvout = 20000 save velocities every 2 ps<br></font><font size="2">nstxtcout = 20000 xtc compressed trajectory output every 2 ps<br>
</font><font size="2">nstenergy = 20000 save energies every 2 ps<br><br></font><font size="2"><br></font><font size="2">nstlog = 20000 update log file every 2 ps<br></font><font size="2">; Bond parameters<br></font><font size="2">continuation = yes Restarting after NPT<br>
</font><font size="2">; Neighborsearching<br></font><font size="2">ns_type = grid search neighboring grid cels<br></font><font size="2">nstlist = 5 10 fs<br></font><font size="2">rlist = 1.0 short-range neighborlist cutoff (in nm)<br>
<br></font><font size="2"><br></font><font size="2">rcoulomb = 1.0 short-range electrostatic cutoff (in nm)<br></font><font size="2">rvdw = 1.0 short-range van der Waals cutoff (in nm)<br></font><font size="2">; Electrostatics<br>
</font><font size="2">coulombtype = PME Particle Mesh Ewald for long-range electrostatics<br></font><font size="2">ewald_rtol = 1e-05<br><br></font><font size="2"><br></font><font size="2">fourierspacing = 0.12 grid spacing for FFT<br>
</font><font size="2">pme_order = 6 ;<br></font><font size="2">; Temperature coupling is on<br></font><font size="2">tcoupl = V-rescale modified Berendsen thermostat<br></font><font size="2">tc-grps = Protein Non-Protein two coupling groups - more accurate<br>
<br></font><font size="2"><br></font><font size="2">tau_t = 0.1 0.1 time constant, in ps<br></font><font size="2">ref_t = 300 300 reference temperature, one for each group, in K<br></font><font size="2">; Pressure coupling is on<br>
</font><font size="2">pcoupl = Parrinello-Rahman Pressure coupling on in NPT<br></font><font size="2">pcoupltype = isotropic uniform scaling of box vectors<br><br></font><font size="2"><br></font><font size="2">tau_p = 1.0 time constant, in ps<br>
</font><font size="2">ref_p = 1.0 reference pressure, in bar<br></font><font size="2">compressibility = 4.5e-5 isothermal compressibility of water, bar^-1<br></font><font size="2">; Periodic boundary conditions<br></font><font size="2">pbc = xyz 3-D PBC<br>
<br></font><font size="2">; Dispersion correction<br><br></font><font size="2">DispCorr = EnerPres account for cut-off vdW scheme<br></font><font size="2">; Velocity generation<br></font><font size="2">gen_vel = no Velocity generation is off<br>
</font><font size="2">morse = yes<br><br><br></font><font size="2">I've searched the net for this error and didn't find any answer. Did anybody see this error? and what should i do with it..<br><br>Thanks,<br>
<br>Michael<br><br></font></div><pre><font size="2"></font></pre></div></div>